Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 17 of 29
Found at i:6205011 original size:108 final size:108
Alignment explanation
Indices: 6204801--6205017 Score: 260
Period size: 108 Copynumber: 2.0 Consensus size: 108
6204791 AGAGCTGATT
* * * * *
6204801 TGCAGTCAGCATTCGTCTGATCTCTCAGTTTACATAATTTTTTCTCATGGTTTGCACCTGGCAAG
1 TGCAGTCAGCATTCATCTCACCTCTCAGTTTACATAATTTTTTCTCATGGTTTGCACCTAGAAAG
* *
6204866 TTATTCTTCTTCACCCATTCAGTTTCATATTGAGCAGGCGATA
66 TTATTCTTCTTCACCCATTCAATTTCATATTCAGCAGGCGATA
* * *
6204909 TGCAGTCAGCATTCATCTCACCTCTCAGTTTACTTGATTTTTTCTCA-GGCTTTGCACTTAGAAA
1 TGCAGTCAGCATTCATCTCACCTCTCAGTTTACATAATTTTTTCTCATGG-TTTGCACCTAGAAA
* * * *
6204973 GTTATTCTTC-TCTATCCAGTT-AATTTCATCTTCTGCAGGTGATA
65 GTTATTCTTCTTC-ACCCA-TTCAATTTCATATTCAGCAGGCGATA
6205017 T
1 T
6205018 AAAAGGTTCT
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
107 4 0.04
108 86 0.93
109 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (108 bp):
TGCAGTCAGCATTCATCTCACCTCTCAGTTTACATAATTTTTTCTCATGGTTTGCACCTAGAAAG
TTATTCTTCTTCACCCATTCAATTTCATATTCAGCAGGCGATA
Found at i:6220575 original size:21 final size:21
Alignment explanation
Indices: 6220549--6220619 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
6220539 AATCTATTAC
6220549 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTGTTTAA
* * ** *
6220570 ATTTAAA-TAAAGATTAATTAC
1 ATTTAAATTTAA-TTTGTTTAA
*
6220591 ATTTAAATTTAATTTGTATAA
1 ATTTAAATTTAATTTGTTTAA
6220612 ATTTAAAT
1 ATTTAAAT
6220620 GAGATATCCT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 3 0.08
21 31 0.84
22 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTTAAATTTAATTTGTTTAA
Found at i:6220865 original size:35 final size:35
Alignment explanation
Indices: 6220813--6220880 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
6220803 CTTATGAAGG
6220813 ACTCTAGTAGTCACTTCATAACAACGACAATGAGA
1 ACTCTAGTAGTCACTTCATAACAACGACAATGAGA
* * *
6220848 ACTCTAGTAG-CTGCTTCATAACAATGAGAATGA
1 ACTCTAGTAGTC-ACTTCATAACAACGACAATGA
6220881 ATAAATCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (35 bp):
ACTCTAGTAGTCACTTCATAACAACGACAATGAGA
Found at i:6232185 original size:30 final size:29
Alignment explanation
Indices: 6232145--6232202 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
6232135 TAAAATAAGT
6232145 ATTTTAATGAAATAAC-AAAACAATTCATAA
1 ATTTTAATGAAA-AACTAAAACAA-TCATAA
* *
6232175 ATTTTGATGAAAAACTAAATCAATCATA
1 ATTTTAATGAAAAACTAAAACAATCATA
6232203 GTTTAAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.31
Consensus pattern (29 bp):
ATTTTAATGAAAAACTAAAACAATCATAA
Found at i:6232397 original size:25 final size:25
Alignment explanation
Indices: 6232351--6232400 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6232341 ATTATGAGAA
*
6232351 TTATAATTATTACTGATGATATTAT
1 TTATAATTATTACTGATCATATTAT
*
6232376 TTATAATTATTTA-TTATCATATTAT
1 TTATAATTA-TTACTGATCATATTAT
6232401 ATGTCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATAATTATTACTGATCATATTAT
Found at i:6241587 original size:2 final size:2
Alignment explanation
Indices: 6241580--6241615 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6241570 AGGTTGTATG
* *
6241580 AT AT AT AT AC AT CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6241616 TTGAAGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6250264 original size:14 final size:14
Alignment explanation
Indices: 6250222--6250264 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
6250212 GGTATGTTTG
6250222 TCATAGATTAAGAA
1 TCATAGATTAAGAA
* *
6250236 TCATATA-T-GGAA
1 TCATAGATTAAGAA
6250248 TCATAGATTAAGAA
1 TCATAGATTAAGAA
6250262 TCA
1 TCA
6250265 GTTTAATGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (14 bp):
TCATAGATTAAGAA
Found at i:6251708 original size:24 final size:24
Alignment explanation
Indices: 6251681--6251746 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
6251671 TTCTCATATT
6251681 CATAACCTCATTTTTGGCATACTC
1 CATAACCTCATTTTTGGCATACTC
6251705 CATAACCTCATTTTTGGCATACTC
1 CATAACCTCATTTTTGGCATACTC
*
6251729 CATAGCCTCATTTTTGGC
1 CATAACCTCATTTTTGGC
6251747 TTTTCTCTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.38
Consensus pattern (24 bp):
CATAACCTCATTTTTGGCATACTC
Found at i:6262759 original size:21 final size:21
Alignment explanation
Indices: 6262733--6262776 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6262723 TGATAATTTG
*
6262733 AATTAAAATAAAAAT-ATAAA
1 AATTTAAATAAAAATAATAAA
* *
6262753 AATTTAATTAAATATAATAAA
1 AATTTAAATAAAAATAATAAA
6262774 AAT
1 AAT
6262777 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTTAAATAAAAATAATAAA
Found at i:6262784 original size:27 final size:25
Alignment explanation
Indices: 6262727--6262793 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 25
6262717 AGGTTTTGAT
*
6262727 AATTTGAATTAAAATAAAAATATAAA
1 AATTT-AATTAAAATAAAAAAATAAA
6262753 AATTTAATTAAATATAATAAAAATAAA
1 AATTTAATTAAA-ATAA-AAAAATAAA
*
6262780 AATTTATTTAAAAT
1 AATTTAATTAAAAT
6262794 CTTTTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 7 0.19
26 11 0.30
27 19 0.51
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (25 bp):
AATTTAATTAAAATAAAAAAATAAA
Found at i:6262829 original size:18 final size:19
Alignment explanation
Indices: 6262795--6262832 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6262785 ATTTAAAATC
*
6262795 TTTTAAATAATTTTAATTT
1 TTTTAAATAATTATAATTT
6262814 TTTTAAAT-ATTATAATTT
1 TTTTAAATAATTATAATTT
6262832 T
1 T
6262833 ATTTTACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAAATAATTATAATTT
Found at i:6283792 original size:35 final size:35
Alignment explanation
Indices: 6283746--6283823 Score: 156
Period size: 35 Copynumber: 2.2 Consensus size: 35
6283736 CAAGGACAAG
6283746 GCCCACTGCCCTAGTTGATGAACATAAATCTAACC
1 GCCCACTGCCCTAGTTGATGAACATAAATCTAACC
6283781 GCCCACTGCCCTAGTTGATGAACATAAATCTAACC
1 GCCCACTGCCCTAGTTGATGAACATAAATCTAACC
6283816 GCCCACTG
1 GCCCACTG
6283824 TTATACTGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.22
Consensus pattern (35 bp):
GCCCACTGCCCTAGTTGATGAACATAAATCTAACC
Found at i:6291975 original size:16 final size:17
Alignment explanation
Indices: 6291954--6291991 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
6291944 TATATTAAAT
6291954 TTAAAT-TAAAAATATA
1 TTAAATATAAAAATATA
*
6291970 TTAAATAATAAAAATATT
1 TTAAAT-ATAAAAATATA
6291988 TTAA
1 TTAA
6291992 TGGAACCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAATATAAAAATATA
Found at i:6292274 original size:29 final size:31
Alignment explanation
Indices: 6292209--6292274 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
6292199 TCAAATCAAG
6292209 TTTTTTAATTTCTTAATTAATCAAAAATATA
1 TTTTTTAATTTCTTAATTAATCAAAAATATA
* * **
6292240 TATTTT-ATTT-TTAATTGATCAAATGTATA
1 TTTTTTAATTTCTTAATTAATCAAAAATATA
6292269 TTTTTT
1 TTTTTT
6292275 TATATCTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 21 0.70
30 4 0.13
31 5 0.17
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTTTAATTTCTTAATTAATCAAAAATATA
Found at i:6310747 original size:2 final size:2
Alignment explanation
Indices: 6310740--6310767 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6310730 CAATCAAGTT
6310740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6310768 ATTGAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6320063 original size:21 final size:22
Alignment explanation
Indices: 6320013--6320063 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
6320003 TATATATAAC
* *
6320013 ATAATATTTTAAAAGGTTTTTGA
1 ATAA-ATTTTAAAAGATTTTTAA
*
6320036 AT-TATTTTAAAA-ATTTTTAA
1 ATAAATTTTAAAAGATTTTTAA
6320056 ATAAATTT
1 ATAAATTT
6320064 CTTTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.35
21 13 0.57
23 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (22 bp):
ATAAATTTTAAAAGATTTTTAA
Found at i:6320113 original size:15 final size:15
Alignment explanation
Indices: 6320095--6320124 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6320085 CAGTTGACTA
6320095 AATGATATTAATTAT
1 AATGATATTAATTAT
*
6320110 AATGATATTTATTAT
1 AATGATATTAATTAT
6320125 TTTATACTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
AATGATATTAATTAT
Found at i:6325473 original size:3 final size:3
Alignment explanation
Indices: 6325465--6325495 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6325455 ATGTGAAGGA
*
6325465 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6325496 CGGTTTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6326512 original size:27 final size:26
Alignment explanation
Indices: 6326482--6326558 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 26
6326472 ACGTCACATC
6326482 GAAGATTTAGTTATTATATATCATGTT
1 GAAGATTTAGTTATTATA-ATCATGTT
* * * *
6326509 GAAGATTTAATTGTTACACT-ATGTT
1 GAAGATTTAGTTATTATAATCATGTT
*
6326534 GAACATTTAGTTATTATACATCATG
1 GAAGATTTAGTTATTATA-ATCATG
6326559 ATAAAAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 19 0.49
26 2 0.05
27 18 0.46
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (26 bp):
GAAGATTTAGTTATTATAATCATGTT
Found at i:6338215 original size:17 final size:18
Alignment explanation
Indices: 6338193--6338226 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6338183 TTCTCTTAAT
6338193 TATAAAA-AAGAAAAAAA
1 TATAAAACAAGAAAAAAA
*
6338210 TATAAAACATGAAAAAA
1 TATAAAACAAGAAAAAA
6338227 TGAAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (18 bp):
TATAAAACAAGAAAAAAA
Found at i:6343880 original size:21 final size:23
Alignment explanation
Indices: 6343856--6343905 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
6343846 TATAAGTAAG
*
6343856 ATTTATAAT-TAT-TATTAAATA
1 ATTTATAATATATATATGAAATA
* *
6343877 ATTTGTAATATATATATGATATA
1 ATTTATAATATATATATGAAATA
6343900 ATTTAT
1 ATTTAT
6343906 CTACTATAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
ATTTATAATATATATATGAAATA
Found at i:6348847 original size:2 final size:2
Alignment explanation
Indices: 6348840--6348871 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6348830 TCAGGCCTGA
6348840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6348872 TGGGTAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6369790 original size:3 final size:3
Alignment explanation
Indices: 6369782--6369811 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6369772 TTAATATGTA
6369782 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6369812 GATTGAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6370963 original size:26 final size:26
Alignment explanation
Indices: 6370927--6370979 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
6370917 ATTTCTATTA
6370927 TTTCTTTTACAACACAAATGTTTTTT
1 TTTCTTTTACAACACAAATGTTTTTT
*
6370953 TTTCTTTTACAACATAAATGTTTTTT
1 TTTCTTTTACAACACAAATGTTTTTT
6370979 T
1 T
6370980 AATTAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTCTTTTACAACACAAATGTTTTTT
Found at i:6371088 original size:65 final size:66
Alignment explanation
Indices: 6370992--6371119 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 66
6370982 TTAAACAAAC
* *
6370992 AAAAAACAAAAGAATTGTCAAAAAAAGTTTTTATTATCTTTTTACACAAAATTAACTGAAAATAC
1 AAAAAACAAAAGAATTATCAAAAAAAGTTTTTATTATCTTTTTACAAAAAATTAACTGAAAATAC
6371057 A
66 A
* *
6371058 AAAAAATAAAAGAATTAT-AAAAAAAGTTTTTATTATCTTTTTATAAAAAATTAACTGAAAAT
1 AAAAAACAAAAGAATTATCAAAAAAAGTTTTTATTATCTTTTTACAAAAAATTAACTGAAAAT
6371120 TTAACACCAT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 42 0.72
66 16 0.28
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (66 bp):
AAAAAACAAAAGAATTATCAAAAAAAGTTTTTATTATCTTTTTACAAAAAATTAACTGAAAATAC
A
Found at i:6373638 original size:7 final size:7
Alignment explanation
Indices: 6373625--6373656 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6373615 CTTGCTCATC
6373625 CCAAAAT
1 CCAAAAT
*
6373632 TCAAAAT
1 CCAAAAT
6373639 CCAAAAT
1 CCAAAAT
6373646 CCAAAAT
1 CCAAAAT
6373653 CCAA
1 CCAA
6373657 GACCTTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (7 bp):
CCAAAAT
Found at i:6374212 original size:23 final size:22
Alignment explanation
Indices: 6374163--6374214 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
6374153 GTCTGCTATG
*
6374163 CTTTCAATTTCTCTCTCTTATA
1 CTTTCAATTTCTCTCTCTTACA
* *
6374185 TTTTCAGATTTCTCTTTCTTACA
1 CTTTCA-ATTTCTCTCTCTTACA
6374208 CTTTCAA
1 CTTTCAA
6374215 GACACCAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.19, C:0.25, G:0.02, T:0.54
Consensus pattern (22 bp):
CTTTCAATTTCTCTCTCTTACA
Found at i:6381886 original size:13 final size:13
Alignment explanation
Indices: 6381868--6381895 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6381858 ATGAAGGATC
6381868 AAGGATTCCCATT
1 AAGGATTCCCATT
6381881 AAGGATTCCCATT
1 AAGGATTCCCATT
6381894 AA
1 AA
6381896 ATCTCATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (13 bp):
AAGGATTCCCATT
Found at i:6395297 original size:18 final size:18
Alignment explanation
Indices: 6395276--6395313 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6395266 TGAACTTAAC
*
6395276 TAATAATCAA-AATATTTA
1 TAATAAACAACAA-ATTTA
6395294 TAATAAACAACAAATTTA
1 TAATAAACAACAAATTTA
6395312 TA
1 TA
6395314 TAACCTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATAAACAACAAATTTA
Found at i:6395788 original size:17 final size:17
Alignment explanation
Indices: 6395766--6395841 Score: 54
Period size: 17 Copynumber: 4.7 Consensus size: 17
6395756 TAATGCATAA
6395766 AATATAAATAGTTAAAT
1 AATATAAATAGTTAAAT
* * *
6395783 AATATATATAG--GATT
1 AATATAAATAGTTAAAT
* *
6395798 CATA-CAAT-GATTAAAT
1 AATATAAATAG-TTAAAT
6395814 -ATATAAATAGTTAAAT
1 AATATAAATAGTTAAAT
*
6395830 AATATGAATAGT
1 AATATAAATAGT
6395842 AAGAAGATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
13 1 0.02
14 2 0.05
15 8 0.19
16 11 0.26
17 21 0.49
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (17 bp):
AATATAAATAGTTAAAT
Found at i:6397126 original size:37 final size:37
Alignment explanation
Indices: 6397074--6397147 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
6397064 AAAAAAGAAG
6397074 ATAAATAAAACTTTACCTCTTTTTAATTTCACACAGT
1 ATAAATAAAACTTTACCTCTTTTTAATTTCACACAGT
*
6397111 ATAAATAAAATTTTACCTCTTTTTAATTTCACACAGT
1 ATAAATAAAACTTTACCTCTTTTTAATTTCACACAGT
6397148 GGTAAGTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.42
Consensus pattern (37 bp):
ATAAATAAAACTTTACCTCTTTTTAATTTCACACAGT
Found at i:6404857 original size:87 final size:87
Alignment explanation
Indices: 6404711--6404878 Score: 257
Period size: 87 Copynumber: 1.9 Consensus size: 87
6404701 AGGGGTGGGG
* *
6404711 CTCCTGGAATAACTACGACGATAATTTCTACTCGGTTCTCTTAATGGACTTCTGCTGATGCTTCT
1 CTCCTGGAATAACTACGACGATAATTTCTACTCGGTTCCCTTAACGGACTTCTGCTGATGCTTCT
* *
6404776 CTTTGGAGGGGCCCTGGCAGGA
66 CCTTGGAGGAGCCCTGGCAGGA
* * *
6404798 CTCCTTGAATAACTATGACGATAA-TTCTTACTTGGTTCCCTTAACGGACTTCTGCTGATGCTTC
1 CTCCTGGAATAACTACGACGATAATTTC-TACTCGGTTCCCTTAACGGACTTCTGCTGATGCTTC
6404862 TCCTTGGAGGAGCCCTG
65 TCCTTGGAGGAGCCCTG
6404879 CCAGAGCTCC
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 3 0.04
87 70 0.96
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (87 bp):
CTCCTGGAATAACTACGACGATAATTTCTACTCGGTTCCCTTAACGGACTTCTGCTGATGCTTCT
CCTTGGAGGAGCCCTGGCAGGA
Found at i:6404939 original size:36 final size:36
Alignment explanation
Indices: 6404897--6405009 Score: 138
Period size: 36 Copynumber: 3.1 Consensus size: 36
6404887 CCTACTTACA
*
6404897 CTTCTCCGAGACGATCTCACAGGGCTTCTGCTTATG
1 CTTCTCCGAGACGATCTCACAGGACTTCTGCTTATG
* * *
6404933 CTTCTCCGAG-CAGATTTTACAGGACTTCTGCTAATG
1 CTTCTCCGAGAC-GATCTCACAGGACTTCTGCTTATG
* * * *
6404969 CTTCTCCGAGAAGATCTCGCTGGACTTCTACTTATG
1 CTTCTCCGAGACGATCTCACAGGACTTCTGCTTATG
6405005 CTTCT
1 CTTCT
6405010 TTTTGAAAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
35 1 0.02
36 63 0.98
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (36 bp):
CTTCTCCGAGACGATCTCACAGGACTTCTGCTTATG
Found at i:6427686 original size:14 final size:15
Alignment explanation
Indices: 6427656--6427698 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
6427646 TAAAAAATAA
6427656 TAATTAA-TATT--T
1 TAATTAATTATTAAT
6427668 TAATTAATTA-TAAT
1 TAATTAATTATTAAT
6427682 TAATTAATTATTAAT
1 TAATTAATTATTAAT
6427697 TA
1 TA
6427699 TAAAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 11 0.41
15 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTAATTATTAAT
Found at i:6427735 original size:20 final size:21
Alignment explanation
Indices: 6427710--6427756 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6427700 AAAATTTATT
6427710 AAATTTAAAATAAA-GT-ATAA
1 AAATTT-AAATAAATGTAATAA
*
6427730 AAATTTAATTAAATGTAATAA
1 AAATTTAAATAAATGTAATAA
6427751 AAATTT
1 AAATTT
6427757 TATTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
AAATTTAAATAAATGTAATAA
Found at i:6432339 original size:73 final size:73
Alignment explanation
Indices: 6432208--6432346 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 73
6432198 TTAATTTATC
* * * *
6432208 TAGGGTTGTGATCAAATACATGTTAGGTGCAAAATTGCAACTCCCCAGTTGGCTTGGCATCCAAA
1 TAGGGTTGTGATCAAATACATGCTAGGTGCAAAATTGCAACTCCCCAATAGGCCTGGCATCCAAA
6432273 ACACTAAT
66 ACACTAAT
* * *
6432281 TAGGGTTGTGATCAAATACGTGCTAGGTGCAAAATTGCAACTCTCCAATAGGCCTGGCATTCAAA
1 TAGGGTTGTGATCAAATACATGCTAGGTGCAAAATTGCAACTCCCCAATAGGCCTGGCATCCAAA
6432346 A
66 A
6432347 AACTTACTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (73 bp):
TAGGGTTGTGATCAAATACATGCTAGGTGCAAAATTGCAACTCCCCAATAGGCCTGGCATCCAAA
ACACTAAT
Found at i:6439055 original size:22 final size:22
Alignment explanation
Indices: 6439030--6439090 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
6439020 AAGCAAATCA
*
6439030 ATTAGTTATTAGGTATTATATT
1 ATTAGTTTTTAGGTATTATATT
*** *
6439052 ATTAGTTTTTAAACATTATCTT
1 ATTAGTTTTTAGGTATTATATT
*
6439074 ACTAGTTTTTAGGTATT
1 ATTAGTTTTTAGGTATT
6439091 GTCTACGCAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (22 bp):
ATTAGTTTTTAGGTATTATATT
Found at i:6439969 original size:23 final size:25
Alignment explanation
Indices: 6439943--6440007 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
6439933 ACATGGCATA
6439943 TAACA-GTTTTTGTA-TATGACATG
1 TAACACGTTTTTGTACTATGACATG
*
6439966 TAACAACCTTTTT-TAACTATGACATG
1 TAAC-ACGTTTTTGT-ACTATGACATG
*
6439992 TAACATGTTTTTGTAC
1 TAACACGTTTTTGTAC
6440008 ATGGTGTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
23 4 0.12
24 2 0.06
25 14 0.41
26 14 0.41
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (25 bp):
TAACACGTTTTTGTACTATGACATG
Found at i:6440003 original size:26 final size:26
Alignment explanation
Indices: 6439919--6440003 Score: 72
Period size: 26 Copynumber: 3.4 Consensus size: 26
6439909 GTGTAACAAC
* *
6439919 AACAT-TTTTTTTCAAC-ATGGCATAT
1 AACATGTTTTTTT-AACTATGACATGT
*
6439944 AACA-GTTTTTGT-A-TATGACATGT
1 AACATGTTTTTTTAACTATGACATGT
***
6439967 AACAACCTTTTTTAACTATGACATGT
1 AACATGTTTTTTTAACTATGACATGT
6439993 AACATGTTTTT
1 AACATGTTTTT
6440004 GTACATGGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
23 12 0.26
24 5 0.11
25 11 0.24
26 18 0.39
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (26 bp):
AACATGTTTTTTTAACTATGACATGT
Found at i:6440046 original size:84 final size:84
Alignment explanation
Indices: 6439958--6440148 Score: 217
Period size: 84 Copynumber: 2.3 Consensus size: 84
6439948 GTTTTTGTAT
* *
6439958 ATGACATGTAACAACCTTTTTTAACTATGACATGTAACATGTTTTTGTACATGGTGTGTAACAAC
1 ATGACATATAACAACCTTTTTTAACTATGACATGTAACATGTTTTTGTACATAGTGTGTAACAAC
6440023 AATATATATATTTTTTAAC
66 AATATATATATTTTTTAAC
* * ** * *** *
6440042 ATGACGTATAATAATTTTTTTTAATTATGGTGTGTAACATGTTTTTGTACATAGTGTGTAACAAT
1 ATGACATATAACAACCTTTTTTAACTATGACATGTAACATGTTTTTGTACATAGTGTGTAACAAC
* *
6440107 AATAT-T-T-TTTGTTCAAT
66 AATATATATATTT-TTTAAC
* *
6440124 ATGACATATAATAACCATTTTTAAC
1 ATGACATATAACAACCTTTTTTAAC
6440149 CAAAGCGTGT
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
81 3 0.03
82 25 0.28
83 1 0.01
84 59 0.67
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (84 bp):
ATGACATATAACAACCTTTTTTAACTATGACATGTAACATGTTTTTGTACATAGTGTGTAACAAC
AATATATATATTTTTTAAC
Found at i:6442637 original size:20 final size:19
Alignment explanation
Indices: 6442604--6442641 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6442594 AAGTAAAAAT
*
6442604 AAAAGAGAAGAGAAAGAGA
1 AAAAAAGAAGAGAAAGAGA
6442623 AAAAAAGAAGAAGAAAGAG
1 AAAAAAGAAG-AGAAAGAG
6442642 GTGTGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAGAGAAAGAGA
Found at i:6442638 original size:79 final size:79
Alignment explanation
Indices: 6442513--6442677 Score: 305
Period size: 79 Copynumber: 2.1 Consensus size: 79
6442503 GAGAAAAGAC
6442513 TAAAGTAAAAATAAAAGAGAAGAGAAAGAGAAAAAAAAAAAAAGAAAGAGGTGTGAAGAAACTTA
1 TAAAGTAAAAATAAAAGAGAAGAGAAAGAGAAAAAAAAAAAAAGAAAGAGGTGTGAAGAAACTTA
6442578 AATTAAGATAAAGT
66 AATTAAGATAAAGT
* *
6442592 TAAAGTAAAAATAAAAGAGAAGAGAAAGAGAAAAAAAGAAGAAGAAAGAGGTGTGAAGAAACTTA
1 TAAAGTAAAAATAAAAGAGAAGAGAAAGAGAAAAAAAAAAAAAGAAAGAGGTGTGAAGAAACTTA
6442657 AATTAAGATAAAGT
66 AATTAAGATAAAGT
6442671 T-AAGTAA
1 TAAAGTAA
6442678 GGTTTATGAG
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
78 6 0.07
79 78 0.93
ACGTcount: A:0.63, C:0.01, G:0.21, T:0.15
Consensus pattern (79 bp):
TAAAGTAAAAATAAAAGAGAAGAGAAAGAGAAAAAAAAAAAAAGAAAGAGGTGTGAAGAAACTTA
AATTAAGATAAAGT
Found at i:6443014 original size:17 final size:17
Alignment explanation
Indices: 6442992--6443027 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
6442982 ATCTTTTATC
6442992 ATGGTGTTTATGTTTTA
1 ATGGTGTTTATGTTTTA
6443009 ATGGTGTTTATGTTTTA
1 ATGGTGTTTATGTTTTA
6443026 AT
1 AT
6443028 TGTGGAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (17 bp):
ATGGTGTTTATGTTTTA
Found at i:6443716 original size:27 final size:27
Alignment explanation
Indices: 6443686--6443749 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
6443676 TTCATATTTC
*
6443686 ATATGCAATTAAATGATTTAAGAGAAA
1 ATATACAATTAAATGATTTAAGAGAAA
*
6443713 ATATAAAATTAAATGATTTAAGAGAAA
1 ATATACAATTAAATGATTTAAGAGAAA
*
6443740 GTATACAATT
1 ATATACAATT
6443750 GATTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (27 bp):
ATATACAATTAAATGATTTAAGAGAAA
Found at i:6443975 original size:92 final size:92
Alignment explanation
Indices: 6443818--6443990 Score: 278
Period size: 92 Copynumber: 1.9 Consensus size: 92
6443808 GCGGATTTTG
* *
6443818 CATAATATCAAGTTTAATGTCATCAATCTTGAATAATTAAATCCATCATTAGGATCAAAAGATGA
1 CATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCCATCATTAGGATCAAAAGATGA
6443883 GTTAAAGAAAAAAAAACATGGATCTCA
66 GTTAAAGAAAAAAAAACATGGATCTCA
* *
6443910 CATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCTAT-ATTTAGGATTAGAAA-AT
1 CATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCCATCA-TTAGGATCA-AAAGAT
6443973 GAGTTAAAGAAAAAAAAA
64 GAGTTAAAGAAAAAAAAA
6443991 GAAAAAAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
91 1 0.01
92 71 0.95
93 3 0.04
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (92 bp):
CATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCCATCATTAGGATCAAAAGATGA
GTTAAAGAAAAAAAAACATGGATCTCA
Found at i:6444092 original size:45 final size:45
Alignment explanation
Indices: 6444032--6444124 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 45
6444022 TTGGGCTAGA
6444032 TGAGCTAAGGAAAAAAAGAAAAAAAGGGAAAAATAATTTCCAAA-TT
1 TGAGCTAAGGAAAAAAAGAAAAAAA-GGAAAAATAATTT-CAAAGTT
*
6444078 TGAGCTAAGGAAAAAAAGGAAAAAAGGAAAAATAATTTCAAAGTT
1 TGAGCTAAGGAAAAAAAGAAAAAAAGGAAAAATAATTTCAAAGTT
6444123 TG
1 TG
6444125 GACTTAAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 4 0.09
45 17 0.38
46 24 0.53
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.18
Consensus pattern (45 bp):
TGAGCTAAGGAAAAAAAGAAAAAAAGGAAAAATAATTTCAAAGTT
Found at i:6482969 original size:2 final size:2
Alignment explanation
Indices: 6482964--6482990 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6482954 CATACAAAAC
6482964 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6482991 ACTGATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6490337 original size:29 final size:29
Alignment explanation
Indices: 6490305--6490360 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
6490295 ATTTAAATAA
6490305 ATTTAAATAAAT-TTTCATATTTTTATTAT
1 ATTTAAATAAATATTT-ATATTTTTATTAT
* *
6490334 ATTTAATTAAATATTTTTATTTTTATT
1 ATTTAAATAAATATTTATATTTTTATT
6490361 TTGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAATATTTATATTTTTATTAT
Found at i:6496260 original size:19 final size:19
Alignment explanation
Indices: 6496226--6496266 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
6496216 AGCTTCTCTT
6496226 TCTAACTTCTCTTCTATTC
1 TCTAACTTCTCTTCTATTC
6496245 TCTAA-TTCTCTATCTATTC
1 TCTAACTTCTCT-TCTATTC
6496264 TCT
1 TCT
6496267 TTAACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTAACTTCTCTTCTATTC
Found at i:6496916 original size:468 final size:470
Alignment explanation
Indices: 6496045--6497147 Score: 1167
Period size: 468 Copynumber: 2.4 Consensus size: 470
6496035 TACTCATTAT
* * * * * * * *
6496045 ATGGGTTACAGTAACAGTTACTCACATTAAAGCTTTTCATAATAATGTTATTTATTACGCGTATT
1 ATGGGTTACAATAACAGTTACTCACATTAAAACTCTTCATAATAATATAATTCATTACACGCATT
*** * * * * * *
6496110 AAAGTTTATTCTTGAGTAATCACCAATT-TTGATACTATATATAGAACCTTCACAATTCATTTGA
66 AAAACCTATTATTGAGTAACCACCACTTCTAG-TACTATATATAGAACCTTCACAACTCA-TTCA
* * * * *
6496174 A-AGATCTTGGCT-TTTTTCAAAGCTATAACCATTCTCACATAAAGC--TTC---------TCT-
129 AGAGATCTTGACTCTTGTCCAAAGCTATAA-CATTCCCACACAAAGCTTTTCTTTTTAAGTTCTC
* * *
6496225 T-TCTAACTTCTCTTCTATTCTCTAATTCTCTATCTATTCTCTTTAACTTTTTCTTGAAATATAA
193 TCTCTAACTTCTCTTCTATTCTCTAATTCTCTACCTATTCTCTTTAACTTTTTCCTGAAATACAA
* * * * * *
6496289 GTGTTTCTTCTTTTTACCTTATTCTCTTGTACCTACTCATGTACACCTTTTTCTTTAAACTTGTT
258 GTGTTTCTGCCTTTTACCTTATTCTCTTATACCTACTCACGTACACCTTTTTCCTTAAACTTATT
* * *
6496354 CTCATATAGCTTTTCATGTGTACCTCTTCTCTATTACTTTTCACTCGAGAACAAGTCTTATTTCA
323 CTCATATAGCTTTTCACGTATACCTCTTCTCTATTACTTTTCACTCGAGAACAAGTCTTATTACA
** * * * ** * ***
6496419 TGCAATTACTTCAACGTTCACAAAATGAGTTTATAATTGTTACTCATTATATGTAATAAAATCAC
388 CCCAATGACATCAAAGTTCACAAAATGAGTTTATAACCGTTACACATTATACACAATAAAATCAC
*
6496484 CATTTTAATATTCACATA
453 CATTTTAATATCCACATA
* * *
6496502 ATGGGTTACAATAACAGTTACTCATATTAAAACTC-TCTATAATAATATAATTCATTGCGCGCAT
1 ATGGGTTACAATAACAGTTACTCACATTAAAACTCTTC-ATAATAATATAATTCATTACACGCAT
*** * * ** * *
6496566 TAAAACCTATTATTGAGTAATTGCCACTTCTGGTATTATATATA-AAGTTTTTACAACTCATTTA
65 TAAAACCTATTATTGAGTAACCACCACTTCTAGTACTATATATAGAA-CCTTCACAACTCATTCA
* * *
6496630 AGAGATCTTGGCTCTTGTCCAGAG-TAATAACATTCTCACACAAAGCTTTTCTTTTTAAGTTCTC
129 AGAGATCTTGACTCTTGTCCAAAGCT-ATAACATTCCCACACAAAGCTTTTCTTTTTAAGTTCTC
* *
6496694 TCTCTAA-TTCTCTTCTATTCTTTAATTCTTTACCTATTCTCTTT-ACTTTTTCCT-AAAGTACA
193 TCTCTAACTTCTCTTCTATTCTCTAATTCTCTACCTATTCTCTTTAACTTTTTCCTGAAA-TACA
* * ** *
6496756 AGTGTTT-TCGCCTTTTATCTTATTCTTTTATACCTGTTCACGTGCACCTTTTTCGCTT-AACTT
257 AGTGTTTCT-GCCTTTTACCTTATTCTCTTATACCTACTCACGTACACCTTTTTC-CTTAAACTT
** * *
6496819 ATTCTTGTATAGCTTTTCACGTATACCTTTTCTCTATTACTTTTTACTCGAGAACAAGTCTTATT
320 ATTCTCATATAGCTTTTCACGTATACCTCTTCTCTATTACTTTTCACTCGAGAACAAGTCTTATT
* * *
6496884 ACACCCAATGACATCAATAG-TCCCATAATGAGTTTTTAACCGTTACACATTATACACAATAAAA
385 ACACCCAATGACATCAA-AGTTCACAAAATGAGTTTATAACCGTTACACATTATACACAATAAAA
6496948 TCACCATTTTAATATCCACATA
449 TCACCATTTTAATATCCACATA
* * * * * *
6496970 ATGGGTTACAGTAACAGTTACTCACATTAAAGCTCTTCATAATAATGTCATTTATTACATGCATT
1 ATGGGTTACAATAACAGTTACTCACATTAAAACTCTTCATAATAATATAATTCATTACACGCATT
* * *
6497035 AAAGCCTATTCTTGAGTAACCACCACTTCTAGTACTATATATAGAACCTTCATAACTCATTCAAG
66 AAAACCTATTATTGAGTAACCACCACTTCTAGTACTATATATAGAACCTTCACAACTCATTCAAG
* *
6497100 AGATCTTGACTCTTTTCCAAAGCTATAACATTCCCACACAGAGCTTTT
131 AGATCTTGACTCTTGTCCAAAGCTATAACATTCCCACACAAAGCTTTT
6497148 TTCTCTAATT
Statistics
Matches: 529, Mismatches: 91, Indels: 41
0.80 0.14 0.06
Matches are distributed among these distances:
456 8 0.02
457 120 0.23
458 13 0.02
459 3 0.01
467 4 0.01
468 333 0.63
469 43 0.08
470 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (470 bp):
ATGGGTTACAATAACAGTTACTCACATTAAAACTCTTCATAATAATATAATTCATTACACGCATT
AAAACCTATTATTGAGTAACCACCACTTCTAGTACTATATATAGAACCTTCACAACTCATTCAAG
AGATCTTGACTCTTGTCCAAAGCTATAACATTCCCACACAAAGCTTTTCTTTTTAAGTTCTCTCT
CTAACTTCTCTTCTATTCTCTAATTCTCTACCTATTCTCTTTAACTTTTTCCTGAAATACAAGTG
TTTCTGCCTTTTACCTTATTCTCTTATACCTACTCACGTACACCTTTTTCCTTAAACTTATTCTC
ATATAGCTTTTCACGTATACCTCTTCTCTATTACTTTTCACTCGAGAACAAGTCTTATTACACCC
AATGACATCAAAGTTCACAAAATGAGTTTATAACCGTTACACATTATACACAATAAAATCACCAT
TTTAATATCCACATA
Found at i:6497849 original size:24 final size:27
Alignment explanation
Indices: 6497822--6497872 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
6497812 TTTGACGAAA
6497822 TTTCCAAC-G-AATT-TCCGTTGGAAT
1 TTTCCAACAGAAATTATCCGTTGGAAT
6497846 TTTCCAACAGAAAATTATCCGTTGGAA
1 TTTCCAACAG-AAATTATCCGTTGGAA
6497873 ATTCATCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.35
25 1 0.04
27 4 0.17
28 10 0.43
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (27 bp):
TTTCCAACAGAAATTATCCGTTGGAAT
Found at i:6505890 original size:35 final size:37
Alignment explanation
Indices: 6505851--6505951 Score: 122
Period size: 35 Copynumber: 2.8 Consensus size: 37
6505841 GTTTTGTATG
*
6505851 AAATAATATTTCACTTGTTTTAATAATT-TT-ACATA
1 AAATAATATTTCACTTGTTATAATAATTGTTAACATA
* *
6505886 AAATAATACTTCACTTGTTATAATTATTGTTCAACATA
1 AAATAATATTTCACTTGTTATAATAATTGTT-AACATA
*
6505924 AAATAATATTTTA--T-TTATAATAATTGTT
1 AAATAATATTTCACTTGTTATAATAATTGTT
6505952 CTTATTATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
35 38 0.67
36 3 0.05
38 16 0.28
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.48
Consensus pattern (37 bp):
AAATAATATTTCACTTGTTATAATAATTGTTAACATA
Found at i:6514379 original size:2 final size:2
Alignment explanation
Indices: 6514372--6514400 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6514362 AGCAAAGCAC
6514372 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6514401 CTGCTAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6518461 original size:19 final size:20
Alignment explanation
Indices: 6518424--6518464 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
6518414 TGAAGGTGAT
6518424 GGAGGAGGTACAGGACGGCG
1 GGAGGAGGTACAGGACGGCG
*
6518444 GGAGGAGG-ACATGACGGCG
1 GGAGGAGGTACAGGACGGCG
6518463 GG
1 GG
6518465 GTAGGCGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.24, C:0.15, G:0.56, T:0.05
Consensus pattern (20 bp):
GGAGGAGGTACAGGACGGCG
Found at i:6519718 original size:71 final size:71
Alignment explanation
Indices: 6519625--6519770 Score: 283
Period size: 71 Copynumber: 2.1 Consensus size: 71
6519615 AGTTAATTGC
*
6519625 TTTATTCATAGAACTTAAAGTTAAGGAGTTGAAATTAATTAGATTAATTTTTAAATATTGTGAGA
1 TTTATTCATAGAACTTAAAGTTAAGGAGTTGAAATTAATTAGACTAATTTTTAAATATTGTGAGA
6519690 CTGGTT
66 CTGGTT
6519696 TTTATTCATAGAACTTAAAGTTAAGGAGTTGAAATTAATTAGACTAATTTTTAAATATTGTGAGA
1 TTTATTCATAGAACTTAAAGTTAAGGAGTTGAAATTAATTAGACTAATTTTTAAATATTGTGAGA
6519761 CTGGTT
66 CTGGTT
6519767 TTTA
1 TTTA
6519771 GGCATTGCAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (71 bp):
TTTATTCATAGAACTTAAAGTTAAGGAGTTGAAATTAATTAGACTAATTTTTAAATATTGTGAGA
CTGGTT
Found at i:6519911 original size:23 final size:23
Alignment explanation
Indices: 6519884--6519943 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
6519874 AGTAATACCT
*
6519884 AAGTCACGCAATGCCTTACTAAC
1 AAGTCACGCAATACCTTACTAAC
* **
6519907 TAGTCACGCAATATGTTACTAAC
1 AAGTCACGCAATACCTTACTAAC
*
6519930 AAGTTACGCAATAC
1 AAGTCACGCAATAC
6519944 TTAAAAGCTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (23 bp):
AAGTCACGCAATACCTTACTAAC
Found at i:6519979 original size:21 final size:21
Alignment explanation
Indices: 6519955--6520012 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
6519945 TAAAAGCTAA
6519955 TCACGCAATGACTAAAGTCAG
1 TCACGCAATGACTAAAGTCAG
* * *
6519976 TCACGCAACGTCCAAAGTCAG
1 TCACGCAATGACTAAAGTCAG
* * *
6519997 TTACGTAATGCCTAAA
1 TCACGCAATGACTAAA
6520013 ATATTAGTCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
TCACGCAATGACTAAAGTCAG
Found at i:6525245 original size:14 final size:15
Alignment explanation
Indices: 6525216--6525248 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6525206 TCTATATTCC
*
6525216 TTTTATTTTTTGCAT
1 TTTTATCTTTTGCAT
6525231 TTTTATCTTTT-CAT
1 TTTTATCTTTTGCAT
6525245 TTTT
1 TTTT
6525249 CATCCACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTATCTTTTGCAT
Found at i:6525394 original size:26 final size:26
Alignment explanation
Indices: 6525365--6525434 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
6525355 ATCCATTCAT
6525365 TTCTAGGGATAAAATTATACATCCAC
1 TTCTAGGGATAAAATTATACATCCAC
** * *
6525391 TTCT-GATAGTAAAATTATTCATCCAT
1 TTCTAGGGA-TAAAATTATACATCCAC
*
6525417 TTCTGATGG-TAAAATTAT
1 TTCT-AGGGATAAAATTAT
6525435 CTTTAATTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (26 bp):
TTCTAGGGATAAAATTATACATCCAC
Found at i:6526699 original size:22 final size:22
Alignment explanation
Indices: 6526672--6526713 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6526662 TTCAAAATAA
6526672 AAATAAA-AATATTTAATTAATT
1 AAATAAATAA-ATTTAATTAATT
*
6526694 AAATAAATAAATTTATTTAA
1 AAATAAATAAATTTAATTAA
6526714 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAAATAAATTTAATTAATT
Found at i:6529590 original size:18 final size:18
Alignment explanation
Indices: 6529564--6529598 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6529554 TGGTGGTGAA
* *
6529564 GAGGTGGAGGAATATGGT
1 GAGGAGGAGGAAGATGGT
6529582 GAGGAGGAGGAAGATGG
1 GAGGAGGAGGAAGATGG
6529599 CAATCATGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.14
Consensus pattern (18 bp):
GAGGAGGAGGAAGATGGT
Found at i:6531187 original size:22 final size:20
Alignment explanation
Indices: 6531155--6531194 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
6531145 TGTTTTGGTT
*
6531155 TTTTAATTAAAGATTAAATA
1 TTTTAATTAAAAATTAAATA
6531175 TTTTAATTGTAAAAATTAAA
1 TTTTAA-T-TAAAAATTAAA
6531195 AAGTAAGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTAATTAAAAATTAAATA
Found at i:6531333 original size:27 final size:27
Alignment explanation
Indices: 6531296--6531358 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
6531286 AATAATTTTA
*
6531296 AAAAATATAATAATATATAT-T-ATATTT
1 AAAAATTTAATAAT-TATATGTCATA-TT
* *
6531323 TAAAATTTAATTATTATATGTCATATT
1 AAAAATTTAATAATTATATGTCATATT
6531350 AAAAATTTA
1 AAAAATTTA
6531359 TATACCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 5 0.17
27 22 0.73
28 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
AAAAATTTAATAATTATATGTCATATT
Found at i:6531361 original size:20 final size:20
Alignment explanation
Indices: 6531336--6531382 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6531326 AATTTAATTA
6531336 TTATATGTCATATTAAAAAT
1 TTATATGTCATATTAAAAAT
** *
6531356 TTATATACCATTTTAAAAAT
1 TTATATGTCATATTAAAAAT
6531376 TTA-ATGT
1 TTATATGT
6531383 TCACATCATG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (20 bp):
TTATATGTCATATTAAAAAT
Found at i:6532307 original size:21 final size:21
Alignment explanation
Indices: 6532281--6532320 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6532271 TACTCCCTCT
*
6532281 CCAATTATATAAAAAAAAACC
1 CCAATTATAAAAAAAAAAACC
6532302 CCAATTATAAAAAAAAAAA
1 CCAATTATAAAAAAAAAAA
6532321 AAAGAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (21 bp):
CCAATTATAAAAAAAAAAACC
Found at i:6537360 original size:21 final size:21
Alignment explanation
Indices: 6537334--6537375 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6537324 ATAAACCGAT
*
6537334 CATAACTCATCTCATTAATGC
1 CATAACTCATCTCACTAATGC
*
6537355 CATAACTCATGTCACTAATGC
1 CATAACTCATCTCACTAATGC
6537376 TCTACAGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (21 bp):
CATAACTCATCTCACTAATGC
Found at i:6543799 original size:24 final size:26
Alignment explanation
Indices: 6543772--6544178 Score: 100
Period size: 26 Copynumber: 15.0 Consensus size: 26
6543762 TATTATAATT
*
6543772 AAAATAAATATATATATAAGA-ATAA
1 AAAATAAATATATATATAAAATATAA
*
6543797 AAATTAAA-ATA-A-ATAAAATATAA
1 AAAATAAATATATATATAAAATATAA
* * *
6543820 AAAATTAATATTTATATAATATAGATAAA
1 AAAATAAATATATATATAA-A-ATAT-AA
* *
6543849 ACAAATTAAA-ATAAAATATATAATATAA
1 A-AAA-TAAATAT-ATATATAAAATATAA
* * *
6543877 AAAAT-AATAAAGAAATGAAAATA-AA
1 AAAATAAATATATATAT-AAAATATAA
*
6543902 ATATATAAA-AT-TATAATAATAA-AT-A
1 A-AAATAAATATATAT-ATAA-AATATAA
* *
6543927 AAAATAAAATATATGACATTAAAAATATATT
1 AAAAT-AAATATAT-ATA-T-AAAATATA-A
*
6543958 AAAATATGATAT-TATATAAAA-ATTAA
1 AAAATA-AATATATATATAAAATA-TAA
* * *
6543984 TATATAAATATAAATATATAAA-ATAA
1 AAAATAAATATATATATA-AAATATAA
*
6544010 AATATAAA-ATAT-TATAATAATA-AA
1 AAAATAAATATATATATAA-AATATAA
*
6544034 TAAAATAAAATAATATGATATTAAAAATATAT
1 -AAAAT-AAAT-ATAT-ATA-T-AAAATATAA
** *
6544066 TTAAGAAATGATATTATATAAAA-ATTAA
1 AAAATAAAT-ATA-TATATAAAATA-TAA
*
6544094 TAATATAAATATAAATATATTAAAA-ATAA
1 -AAAATAAATAT--ATATA-TAAAATATAA
*
6544123 AAATATAAA-ATAT-TATAATAATAAATA
1 AAA-ATAAATATATATATAA-AATATA-A
6544150 AAAATAAAATATATGATATTAAAAATATA
1 AAAAT-AAATATAT-ATA-T-AAAATATA
6544179 TTTAAGAAAT
Statistics
Matches: 280, Mismatches: 45, Indels: 108
0.65 0.10 0.25
Matches are distributed among these distances:
22 5 0.02
23 12 0.04
24 19 0.07
25 42 0.15
26 50 0.18
27 26 0.09
28 31 0.11
29 30 0.11
30 29 0.10
31 31 0.11
32 5 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAATAAATATATATATAAAATATAA
Found at i:6543827 original size:54 final size:57
Alignment explanation
Indices: 6543768--6543881 Score: 139
Period size: 54 Copynumber: 2.1 Consensus size: 57
6543758 ATAATATTAT
*
6543768 AATTAAAATAAATATATATATAAGA-ATAA-AAATTAAAAT-AAATA-A-AATATAAAA
1 AATTAAAATAAATATA-ATAT-AGATAAAACAAATTAAAATAAAATATATAATATAAAA
* **
6543822 AATTAATATTTATATAATATAGATAAAACAAATTAAAATAAAATATATAATATAAAA
1 AATTAAAATAAATATAATATAGATAAAACAAATTAAAATAAAATATATAATATAAAA
6543879 AAT
1 AAT
6543882 AATAAAGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
52 3 0.06
53 7 0.14
54 23 0.45
55 5 0.10
56 1 0.02
57 12 0.24
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (57 bp):
AATTAAAATAAATATAATATAGATAAAACAAATTAAAATAAAATATATAATATAAAA
Found at i:6543871 original size:33 final size:33
Alignment explanation
Indices: 6543832--6543940 Score: 94
Period size: 33 Copynumber: 3.2 Consensus size: 33
6543822 AATTAATATT
* *
6543832 TATATAATATAGATAAAACAAATTAAAATAAAA
1 TATATAATATAAATAAAACAAATAAAAATAAAA
* *
6543865 TATATAATATAAAAAATAATAAAGAAATGAAAATAAAA
1 TATATAATAT---AAAT-A-AAACAAATAAAAATAAAA
* * *
6543903 TATATAAAAT-TATAATAATAAATAAAAATAAAA
1 TATATAATATAAATAA-AACAAATAAAAATAAAA
6543936 TATAT
1 TATAT
6543941 GACATTAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
32 1 0.02
33 31 0.49
34 2 0.03
36 3 0.05
37 1 0.02
38 25 0.40
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (33 bp):
TATATAATATAAATAAAACAAATAAAAATAAAA
Found at i:6543875 original size:38 final size:37
Alignment explanation
Indices: 6543833--6543940 Score: 100
Period size: 38 Copynumber: 3.0 Consensus size: 37
6543823 ATTAATATTT
*
6543833 ATATAATATAGATAAAACAAATTAAAATAAAATATATA
1 ATATAATATA-ATAAAACAAATAAAAATAAAATATATA
* * *
6543871 ATATAA-AAAATAATAAAGAAATGAAAATAAAATATATA
1 ATATAATATAAT-A-AAACAAATAAAAATAAAATATATA
* *
6543909 A-A-ATTATAAT--AATAAATAAAAATAAAATATAT
1 ATATAATATAATAAAACAAATAAAAATAAAATATAT
6543941 GACATTAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
33 20 0.33
36 3 0.05
37 8 0.13
38 29 0.48
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (37 bp):
ATATAATATAATAAAACAAATAAAAATAAAATATATA
Found at i:6543962 original size:31 final size:33
Alignment explanation
Indices: 6543857--6544045 Score: 122
Period size: 32 Copynumber: 5.5 Consensus size: 33
6543847 AAACAAATTA
* *
6543857 AAATAAAATATATAATATA-AAAA--ATAATAAAG
1 AAATAAAA-ATAAAATATATAAAATTATAAT-AAT
*
6543889 AAATGAAAATAAAATATATAAAATTATAATAAT
1 AAATAAAAATAAAATATATAAAATTATAATAAT
* *
6543922 AAATAAAAATAAAATATATGACATTA-AA-AAT
1 AAATAAAAATAAAATATATAAAATTATAATAAT
* * *
6543953 ATATTAAAATATGATATTATATAAAAATTAATATATAAATAT
1 A-AATAAAA-AT-AAAATATAT-AAAATT-ATA-AT--A-AT
6543995 AAATATATAAAATAAAATATA-AAATATTATAATAAT
1 -AA-ATA-AAAATAAAATATATAAA-ATTATAATAAT
6544031 AAAT-AAAATAAAATA
1 AAATAAAAATAAAATA
6544046 ATATGATATT
Statistics
Matches: 125, Mismatches: 14, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
31 13 0.10
32 30 0.24
33 27 0.22
34 14 0.11
35 6 0.05
36 3 0.02
37 2 0.02
38 1 0.01
39 2 0.02
40 6 0.05
41 4 0.03
42 9 0.07
43 5 0.04
44 3 0.02
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAT
Found at i:6544001 original size:28 final size:28
Alignment explanation
Indices: 6543970--6544228 Score: 109
Period size: 28 Copynumber: 9.2 Consensus size: 28
6543960 AATATGATAT
6543970 TATATAAAAATTAATATATAAATATAAA
1 TATATAAAAATTAATATATAAATATAAA
* *
6543998 TATAT-AAAA-TAAAATATAAA-AT-AT
1 TATATAAAAATTAATATATAAATATAAA
6544022 TATAATAATAAA-TAA-A-ATAAA-ATAATA
1 TAT-ATAA-AAATTAATATATAAATATAA-A
* * *
6544049 TGATATTAAAAA-T-ATATTTAAGAAATGATAT
1 T-ATA-TAAAAATTAATATATAA-ATAT-A-AA
6544080 TATATAAAAATTAATAATATAAATATAAA
1 TATATAAAAATTAAT-ATATAAATATAAA
* * *
6544109 TATATTAAAAATAAAAATATAAA-AT-AT
1 TATA-TAAAAATTAATATATAAATATAAA
* * *
6544136 TATAATAATAAATAAAAATA-AAATATATGA
1 TAT-ATAA-AAATTAATATATAAATATA-AA
* * *
6544166 TAT-TAAAAA-T-ATATTTAAGAAATGATAT
1 TATATAAAAATTAATATATAA-ATAT-A-AA
*
6544194 TATATAAAAATTAATAATAAAAATTATAAA
1 TATATAAAAATTAAT-ATATAAA-TATAAA
6544224 TATAT
1 TATAT
6544229 TAAACTTATA
Statistics
Matches: 178, Mismatches: 23, Indels: 58
0.69 0.09 0.22
Matches are distributed among these distances:
24 4 0.02
25 14 0.08
26 16 0.09
27 33 0.19
28 37 0.21
29 25 0.14
30 26 0.15
31 11 0.06
32 12 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
TATATAAAAATTAATATATAAATATAAA
Found at i:6544011 original size:50 final size:50
Alignment explanation
Indices: 6543957--6544228 Score: 161
Period size: 57 Copynumber: 4.9 Consensus size: 50
6543947 AAAAATATAT
6543957 TAAAATATGATATTATATAAAAATTAATATATAAATATAAATATATAAA-A
1 TAAAATATGATATTATATAAAAATTAATATA-AAATATAAATATATAAATA
* * * *
6544007 TAAAATATAAAATATTATAATAATAAA-TAAAATAAAATAATATGATATTAAAAATA
1 TAAAATAT--GATATTAT-ATAA-AAATTAATATAAAAT-ATA-AATA-TATAAATA
* *
6544063 TATTTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAA
1 TA---AA-ATATGATATTATATAAAAATTAAT-ATA-AAATATAAATATA-TAAATA
* * * * *
6544120 TAAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATA
1 T-AAAATAT--GATATTAT-ATAA-AAATTAATATAAAATATA-AATA-TATAAATA
*
6544177 TATTTAAGAAATGATATTATATAAAAATTAATAATAAAAATTATAAATATAT
1 TA---AA-ATATGATATTATATAAAAATTAAT-AT-AAAA-TATAAATATAT
6544229 TAAACTTATA
Statistics
Matches: 169, Mismatches: 23, Indels: 53
0.69 0.09 0.22
Matches are distributed among these distances:
50 8 0.05
52 11 0.07
53 13 0.08
54 9 0.05
55 7 0.04
56 29 0.17
57 38 0.22
58 36 0.21
59 12 0.07
60 6 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (50 bp):
TAAAATATGATATTATATAAAAATTAATATAAAATATAAATATATAAATA
Found at i:6544036 original size:20 final size:21
Alignment explanation
Indices: 6543981--6544048 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 21
6543971 ATATAAAAAT
6543981 TAATATATAAATATAAATATATA
1 TAATA-ATAAATA-AAATATATA
*
6544004 AAATAA-AATATAAAATAT-TA
1 TAATAATAA-ATAAAATATATA
*
6544024 TAATAATAAATAAAATA-AAA
1 TAATAATAAATAAAATATATA
6544044 TAATA
1 TAATA
6544049 TGATATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 21 0.54
21 10 0.26
22 4 0.10
23 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAATAATAAATAAAATATATA
Found at i:6544043 original size:114 final size:112
Alignment explanation
Indices: 6543894--6544228 Score: 556
Period size: 114 Copynumber: 3.0 Consensus size: 112
6543884 TAAAGAAATG
*
6543894 AAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATA-T
1 AAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
6543957 TAA-AATATGATATTATATAAAAATTAAT-ATATAAATATAAATATAT-
65 TAAGAA-ATGATATTATATAAAAATTAATAATATAAATATAAATATATA
6544003 AAAATAAAATATAAAATATTATAATAATAAAT-AAAATAAAATAATATGATATTAAAAATATATT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAAT-ATATGATATTAAAAATATATT
6544067 TAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
65 TAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATA-TA
6544116 AAAATAAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
1 AAAAT-AAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
*
6544181 TAAGAAATGATATTATATAAAAATTAATAATAAAAATTATAAATATAT
65 TAAGAAATGATATTATATAAAAATTAATAATATAAA-TATAAATATAT
6544229 TAAACTTATA
Statistics
Matches: 214, Mismatches: 2, Indels: 15
0.93 0.01 0.06
Matches are distributed among these distances:
108 13 0.06
109 46 0.21
110 26 0.12
111 19 0.09
112 1 0.00
113 5 0.02
114 84 0.39
115 20 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (112 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATA
Found at i:6544090 original size:16 final size:15
Alignment explanation
Indices: 6543932--6544217 Score: 72
Period size: 16 Copynumber: 19.3 Consensus size: 15
6543922 AAATAAAAAT
* *
6543932 AAAATATATGACATTA
1 AAAATATATTATA-TA
6543948 AAAATATA-T-TA-A
1 AAAATATATTATATA
*
6543960 AATATGATATTATATA
1 AAAAT-ATATTATATA
*
6543976 AAAATTAATATATAAATA
1 AAAA-T-ATAT-TATATA
* * *
6543994 TAAATATATAAAATA
1 AAAATATATTATATA
* *
6544009 AAATATAAAATATTATA
1 AAA-ATATATTA-TATA
* * * *
6544026 ATAATAAATAAAAT-
1 AAAATATATTATATA
*
6544040 AAAATAATATGATATTA
1 AAAAT-ATATTATA-TA
6544057 AAAATATATT-TA-A
1 AAAATATATTATATA
*
6544070 GAAATGATATTATATA
1 AAAAT-ATATTATATA
*
6544086 AAAAT-TAATA-ATA
1 AAAATATATTATATA
* *
6544099 TAAATATAAATATATTA
1 AAAATAT-ATTATA-TA
*
6544116 AAAATA-A--AAATA
1 AAAATATATTATATA
*
6544128 TAAA-ATATTATAATA
1 AAAATATATTAT-ATA
*
6544143 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
*
6544155 AAAATATATGATATTA
1 AAAATATATTATA-TA
6544171 AAAATATATT-TA-A
1 AAAATATATTATATA
*
6544184 GAAATGATATTATATA
1 AAAAT-ATATTATATA
*
6544200 AAAAT-TAATA-ATA
1 AAAATATATTATATA
6544213 AAAAT
1 AAAAT
6544218 TATAAATATA
Statistics
Matches: 201, Mismatches: 37, Indels: 67
0.66 0.12 0.22
Matches are distributed among these distances:
11 6 0.03
12 13 0.06
13 32 0.16
14 29 0.14
15 33 0.16
16 56 0.28
17 24 0.12
18 8 0.04
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:6544104 original size:64 final size:63
Alignment explanation
Indices: 6544027--6544214 Score: 206
Period size: 55 Copynumber: 3.2 Consensus size: 63
6544017 AATATTATAA
6544027 TAATAAATAAAATAAAATAATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
1 TAATAAAT-AAATAAAATAATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
* ** * *
6544091 TAAT-AAT--ATAAATATAA-AT-ATATTAAAAATAAAAAT-ATAAA--ATA-T-TATAATAAT
1 TAATAAATAAATAAA-ATAATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
*
6544145 AAAT-AA-AAATAAAAT-ATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
1 TAATAAATAAATAAAATAATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
6544205 TAAT-AATAAA
1 TAATAAATAAA
6544215 AATTATAAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
53 1 0.01
54 17 0.17
55 20 0.20
56 7 0.07
58 7 0.07
59 15 0.15
60 20 0.20
61 7 0.07
63 3 0.03
64 4 0.04
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (63 bp):
TAATAAATAAATAAAATAATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
Found at i:6544106 original size:6 final size:6
Alignment explanation
Indices: 6544095--6544162 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
6544085 AAAAATTAAT
* * *
6544095 AATATA AATATA AATAT- ATTAAA AATAAA AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
6544146 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
6544163 TGATATTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
5 8 0.16
6 27 0.53
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:6544396 original size:15 final size:15
Alignment explanation
Indices: 6544374--6544418 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
6544364 ATGTTATTTT
6544374 CCTGTAATCACATTG
1 CCTGTAATCACATTG
* *
6544389 CTTGTAATCACATTA
1 CCTGTAATCACATTG
6544404 CCTGTAATCACATTG
1 CCTGTAATCACATTG
6544419 TATTGTAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (15 bp):
CCTGTAATCACATTG
Found at i:6550276 original size:30 final size:33
Alignment explanation
Indices: 6550216--6550277 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
6550206 TACATAGTTA
6550216 TATGAAAATAAGAGAAAATAGATATTTATTAAG
1 TATGAAAATAAGAGAAAATAGATATTTATTAAG
* *
6550249 TATGAAAA-AA-ATAAAATATAT-TTTATTAA
1 TATGAAAATAAGAGAAAATAGATATTTATTAA
6550278 TTATTTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 8 0.30
31 9 0.33
32 2 0.07
33 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (33 bp):
TATGAAAATAAGAGAAAATAGATATTTATTAAG
Found at i:6550314 original size:21 final size:22
Alignment explanation
Indices: 6550290--6550332 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6550280 ATTTTAGTTT
*
6550290 TTATATTTTTA-ATAAAATTAA
1 TTATATTATTACATAAAATTAA
6550311 TTATATTATTACTATAAAATTA
1 TTATATTATTAC-ATAAAATTA
6550333 TAAGATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATATTATTACATAAAATTAA
Found at i:6552407 original size:29 final size:28
Alignment explanation
Indices: 6552351--6552433 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 28
6552341 CAAAAACATA
6552351 TTACATGCCATGTTAAACAAAATATTATTG
1 TTACATGCCATGTT-AA-AAAATATTATTG
* *
6552381 TTGCATGCAATGTTCAAAAAATATTATTG
1 TTACATGCCATGTT-AAAAAATATTATTG
* *
6552410 TTACATACCATGTTTAAAAATATT
1 TTACATGCCATGTTAAAAAATATT
6552434 TTATTATACT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
28 9 0.20
29 23 0.50
30 14 0.30
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
TTACATGCCATGTTAAAAAATATTATTG
Found at i:6553802 original size:26 final size:25
Alignment explanation
Indices: 6553773--6553828 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
6553763 TTTTTTGTTT
* *
6553773 ATTTATTTATCTAATAAAATATTAAA
1 ATTTAATTATATAA-AAAATATTAAA
*
6553799 ATTTTAATTATATAACAAATATTAAA
1 A-TTTAATTATATAAAAAATATTAAA
6553825 ATTT
1 ATTT
6553829 TAAATAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.12
26 12 0.46
27 11 0.42
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTAATTATATAAAAAATATTAAA
Found at i:6555520 original size:18 final size:18
Alignment explanation
Indices: 6555497--6555531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6555487 GAAGAGAATA
6555497 AGAAGAGAATTAAAGAGT
1 AGAAGAGAATTAAAGAGT
*
6555515 AGAAGAGAATTAGAGAG
1 AGAAGAGAATTAAAGAG
6555532 ACAGCTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.14
Consensus pattern (18 bp):
AGAAGAGAATTAAAGAGT
Found at i:6560377 original size:20 final size:20
Alignment explanation
Indices: 6560349--6560391 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6560339 ATTGTTTCTT
* *
6560349 AGCCTTAAACTAGACAGG-CA
1 AGCCATAAAC-AGAAAGGACA
6560369 AGCCATAAACAGAAAGGACA
1 AGCCATAAACAGAAAGGACA
6560389 AGC
1 AGC
6560392 TGTAGTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (20 bp):
AGCCATAAACAGAAAGGACA
Found at i:6574740 original size:18 final size:18
Alignment explanation
Indices: 6574714--6574760 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
6574704 AAGTGGTGTC
*
6574714 ATAACTAAAATAATA-ATA
1 ATAATTAAAATAATATA-A
6574732 ATAATTAAAA-AATATAA
1 ATAATTAAAATAATATAA
6574749 ATATATTAAAAT
1 ATA-ATTAAAAT
6574761 CCATAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATTAAAATAATATAA
Found at i:6577300 original size:45 final size:45
Alignment explanation
Indices: 6577196--6577300 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
6577186 TACGTCAGGA
* * * *
6577196 TGTTACACACCGTATACAAAAACATGTTACACGCCATGGTTAGGT
1 TGTTACACACCATGTACAAAAACATGTGACACGCCATGGTTAAGT
** * *
6577241 TGTTACACGTCATGTACAAAAACGTGTGACATGCCATGGTTAAGT
1 TGTTACACACCATGTACAAAAACATGTGACACGCCATGGTTAAGT
6577286 TGTTACACACCATGT
1 TGTTACACACCATGT
6577301 TAAAAAAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (45 bp):
TGTTACACACCATGTACAAAAACATGTGACACGCCATGGTTAAGT
Found at i:6577401 original size:29 final size:31
Alignment explanation
Indices: 6577336--6577403 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 31
6577326 TACAAAAACA
*
6577336 TGTTACACGCCATGGTTAAAAAAAATATTAT
1 TGTTACACACCATGGTTAAAAAAAATATTAT
* * *
6577367 TATTACACACCAT-GTT-GAAAAAATATTGT
1 TGTTACACACCATGGTTAAAAAAAATATTAT
6577396 TGTTACAC
1 TGTTACAC
6577404 GTCATATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 18 0.56
30 3 0.09
31 11 0.34
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (31 bp):
TGTTACACACCATGGTTAAAAAAAATATTAT
Found at i:6577416 original size:29 final size:28
Alignment explanation
Indices: 6577355--6577430 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
6577345 CCATGGTTAA
* * *
6577355 AAAAAATATTATTATTACACACCATGTTG
1 AAAAAATATT-TTGTTACACACCATATTC
**
6577384 AAAAAATATTGTTGTTACACGTCATATTC
1 AAAAAATATT-TTGTTACACACCATATTC
*
6577413 -AAAAACATTTTGTTACAC
1 AAAAAATATTTTGTTACAC
6577431 TTTAATGCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.22
28 8 0.20
29 23 0.57
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (28 bp):
AAAAAATATTTTGTTACACACCATATTC
Found at i:6580225 original size:98 final size:94
Alignment explanation
Indices: 6580123--6580430 Score: 400
Period size: 98 Copynumber: 3.2 Consensus size: 94
6580113 TTTTGTCACT
* * * * *
6580123 ATATTTTGATTTTAATTGATTTAGATTTACTTTAATTGAAAAGGAATATTTCATTTTAATAAAAT
1 ATATTTTGATTTTAAGTGATTTAGATATAATTTAATTGAAAA-GAATATTCCTTTTTAATAAAAT
* *
6580188 AATAAATTTCATAATATCACATCCAATATTAAA
65 AATAAATTTAATAATAT-A-AT-AAATATTAAA
* * * *
6580221 ATATTTTGAATTTCAGTAATTTAGATATAATTTAATTAGAAAAAAATATTCCTTTTTAATAAAAT
1 ATATTTTGATTTTAAGTGATTTAGATATAATTTAATT-GAAAAGAATATTCCTTTTTAATAAAAT
6580286 AATAAATTTAATAATATAAAATAAAATATTAAA
65 AATAAATTTAATAATAT--AAT-AAATATTAAA
* * *
6580319 CTACTTTGATTTTAAGTGATTTAGATATAATTTAATTAAAAAAGAATATTCCTTTTTAATAAAAT
1 ATATTTTGATTTTAAGTGATTTAGATATAATTTAATT-GAAAAGAATATTCCTTTTTAATAAAAT
6580384 AATAAATTTAATAATATAATAAATATTAAA
65 AATAAATTTAATAATATAATAAATATTAAA
*
6580414 ATATTTTAATTTTAAGT
1 ATATTTTGATTTTAAGT
6580431 TGGAACTTTA
Statistics
Matches: 185, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
95 24 0.13
96 3 0.02
98 152 0.82
99 6 0.03
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (94 bp):
ATATTTTGATTTTAAGTGATTTAGATATAATTTAATTGAAAAGAATATTCCTTTTTAATAAAATA
ATAAATTTAATAATATAATAAATATTAAA
Found at i:6580416 original size:17 final size:17
Alignment explanation
Indices: 6580373--6580417 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
6580363 AATATTCCTT
*
6580373 TTTAATAAAATAATAAA
1 TTTAATAATATAATAAA
6580390 TTTAATAATATAATAAA
1 TTTAATAATATAATAAA
6580407 TATTAA-AATAT
1 T-TTAATAATAT
6580418 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAATAATATAATAAA
Found at i:6583372 original size:167 final size:167
Alignment explanation
Indices: 6583090--6583403 Score: 517
Period size: 167 Copynumber: 1.9 Consensus size: 167
6583080 CAGCCGATTA
*
6583090 AATTAATAAAGTTTCATTTATATATTGTGAATCTCAAGTAAATTAAACTAAATATGACGTATATA
1 AATTAATAAAGTTTCATATATATATTGTGAATCTCAAGTAAATTAAACTAAATATGACGTATATA
6583155 TGTGAGATTGTCACTTATGACTTCTCCCCAAACACACCTTTCAATTTTAATTAATTATAAGCC-C
66 TGTGAGATTGTCACTTATGACTTCTCCCCAAACACACCTTTCAATTTTAATTAATTATAAGCCTC
*
6583219 TAATCTAATATAATTAGAGCCTTTACTTGATCTTAGTC
131 -AATATAATATAATTAGAGCCTTTACTTGATCTTAGTC
*
6583257 AATTAATAAAGTTT-A-ATATATATTGTGAATCTCAAGTAAATTAAATTAAATATGACAAGTATA
1 AATTAATAAAGTTTCATATATATATTGTGAATCTCAAGTAAATTAAACTAAATATGAC--GTATA
* * *
6583320 TATGTGAGATTGTCACTTATGATTTCTCCCCAAACACACCTTTCATTTTTAATTAATTGTAAGCC
64 TATGTGAGATTGTCACTTATGACTTCTCCCCAAACACACCTTTCAATTTTAATTAATTATAAGCC
*
6583385 TCAGTATAATATAATTAGA
129 TCAATATAATATAATTAGA
6583404 AATTGGGTAG
Statistics
Matches: 137, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
165 39 0.28
166 1 0.01
167 96 0.70
168 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (167 bp):
AATTAATAAAGTTTCATATATATATTGTGAATCTCAAGTAAATTAAACTAAATATGACGTATATA
TGTGAGATTGTCACTTATGACTTCTCCCCAAACACACCTTTCAATTTTAATTAATTATAAGCCTC
AATATAATATAATTAGAGCCTTTACTTGATCTTAGTC
Found at i:6598305 original size:43 final size:43
Alignment explanation
Indices: 6598244--6598329 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
6598234 TCTCTGGCAG
6598244 TTGTAACAAGTTAATAGGGAATTAGTTGAGTCTGGAAAGAAAA
1 TTGTAACAAGTTAATAGGGAATTAGTTGAGTCTGGAAAGAAAA
6598287 TTGTAACAAGTTAATAGGGAATTAGTTGAGTCTGGAAAGAAAA
1 TTGTAACAAGTTAATAGGGAATTAGTTGAGTCTGGAAAGAAAA
6598330 GAAGCCAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.28
Consensus pattern (43 bp):
TTGTAACAAGTTAATAGGGAATTAGTTGAGTCTGGAAAGAAAA
Found at i:6603711 original size:36 final size:36
Alignment explanation
Indices: 6603641--6603711 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
6603631 ACTCGTTTAA
* * * *
6603641 TTAATCGTGTTATCGTGTTTATACGTATAAACGTGT
1 TTAATCGTGTTATCATGTCTAAACATATAAACGTGT
* *
6603677 TTAATTGTGTTATCATGTCTAAACATATATACGTG
1 TTAATCGTGTTATCATGTCTAAACATATAAACGTG
6603712 ATACATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (36 bp):
TTAATCGTGTTATCATGTCTAAACATATAAACGTGT
Found at i:6603975 original size:9 final size:9
Alignment explanation
Indices: 6603958--6603988 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6603948 ATATTTTTAT
*
6603958 TTAATTGTG
1 TTAAATGTG
6603967 TTAAATGTG
1 TTAAATGTG
6603976 TTAAATGTG
1 TTAAATGTG
6603985 TTAA
1 TTAA
6603989 TCATGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (9 bp):
TTAAATGTG
Found at i:6605276 original size:15 final size:16
Alignment explanation
Indices: 6605249--6605279 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6605239 ACCGATTCTC
6605249 TCAAGATTTAGGGTTT
1 TCAAGATTTAGGGTTT
6605265 TCAAGA-TTAGGGTTT
1 TCAAGATTTAGGGTTT
6605280 AGAAAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (16 bp):
TCAAGATTTAGGGTTT
Found at i:6610169 original size:2 final size:2
Alignment explanation
Indices: 6610162--6610204 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
6610152 ACAACCATGC
*
6610162 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6610204 A
1 A
6610205 CTTAGACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6619037 original size:13 final size:12
Alignment explanation
Indices: 6619012--6619036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6619002 AGTTTCTTTC
6619012 TGAAACTTTTTT
1 TGAAACTTTTTT
6619024 TGAAACTTTTTT
1 TGAAACTTTTTT
6619036 T
1 T
6619037 TTAGATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TGAAACTTTTTT
Found at i:6621174 original size:2 final size:2
Alignment explanation
Indices: 6621167--6621197 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6621157 GATGTTAAGA
6621167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6621198 AGTGTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6623310 original size:22 final size:21
Alignment explanation
Indices: 6623264--6623304 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
6623254 GAATAAAATG
6623264 ATAATTAATATTATAATTTAAA
1 ATAATTAATATTAT-ATTTAAA
6623286 ATAATTAATTATTAT-TTTA
1 ATAATTAA-TATTATATTTA
6623305 TTAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAATTAATATTATATTTAAA
Found at i:6628539 original size:29 final size:28
Alignment explanation
Indices: 6628489--6628580 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
6628479 GGCATTAAAA
*
6628489 TGTAACAA-AATATTTTTAAATATGACG
1 TGTAACAATAATATTTTTTAATATGACG
* * *
6628516 TGTAATAATAATATTTTTTTAATATTACA
1 TGTAACAATAATA-TTTTTTAATATGACG
* * *
6628545 CGTAACAATAATAATTTTCTAACATGACG
1 TGTAACAATAAT-ATTTTTTAATATGACG
6628574 TGTAACA
1 TGTAACA
6628581 TGTTTTTGTA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
27 7 0.14
28 4 0.08
29 39 0.76
30 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (28 bp):
TGTAACAATAATATTTTTTAATATGACG
Found at i:6628654 original size:26 final size:25
Alignment explanation
Indices: 6628612--6628686 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 25
6628602 ACAATAATTT
*
6628612 TTTTTCAAC-ATAACGTGTAACAACTA
1 TTTTT-AACTATAGCGTGTAA-AACTA
* *
6628638 TTTTTAACTATAGCGTGTAATA-TG
1 TTTTTAACTATAGCGTGTAAAACTA
6628662 TTTTTATA-TATAGCGTGTAAGAACT
1 TTTTTA-ACTATAGCGTGTAA-AACT
6628687 TAACTATAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 19 0.46
25 6 0.15
26 16 0.39
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (25 bp):
TTTTTAACTATAGCGTGTAAAACTA
Found at i:6629812 original size:2 final size:2
Alignment explanation
Indices: 6629807--6629836 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6629797 TTTACTAAGG
6629807 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6629837 GTAGTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6631830 original size:74 final size:73
Alignment explanation
Indices: 6631678--6631834 Score: 217
Period size: 74 Copynumber: 2.1 Consensus size: 73
6631668 AAACTTATAC
* * *
6631678 TTATAAATATATATTCATTAAACGAAGATCATTGAAATATTTCTTATTATAATTATTAGTGAGGT
1 TTATAAATATATATTCATCAAACGAAGATCATTGAAATATTTCTTATTATAATTATTAGTAAGAT
6631743 TTAAATTTA
66 TT-AATTTA
* * * *
6631752 TTATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATATATTCATCAAACGAAGATCATTGAAATATTTCTTATTATAATTATTAGTAAGAT
6631817 TT-ATTCTA
66 TTAATT-TA
6631825 TTTATAAATA
1 -TTATAAATA
6631835 AAAATTTAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
72 3 0.04
73 2 0.03
74 69 0.93
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (73 bp):
TTATAAATATATATTCATCAAACGAAGATCATTGAAATATTTCTTATTATAATTATTAGTAAGAT
TTAATTTA
Found at i:6631951 original size:21 final size:21
Alignment explanation
Indices: 6631927--6631966 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6631917 TAAATTATTT
6631927 TTTTAAAATTAAATATTTTTA
1 TTTTAAAATTAAATATTTTTA
***
6631948 TTTTATTTTTAAATATTTT
1 TTTTAAAATTAAATATTTT
6631967 AATTAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAAAATTAAATATTTTTA
Found at i:6633740 original size:4 final size:4
Alignment explanation
Indices: 6633733--6633757 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6633723 TTTGTAACTA
6633733 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
6633758 CAGGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:6634094 original size:2 final size:2
Alignment explanation
Indices: 6634081--6634116 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6634071 TAACGCCTTC
* *
6634081 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6634117 TACTGGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6643605 original size:17 final size:18
Alignment explanation
Indices: 6643574--6643607 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6643564 TTGGCTAGTC
6643574 TATTTAAATTATATTTAT
1 TATTTAAATTATATTTAT
6643592 TATTTAAA-TATATTTA
1 TATTTAAATTATATTTA
6643608 CATTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTAAATTATATTTAT
Found at i:6643614 original size:17 final size:18
Alignment explanation
Indices: 6643574--6643616 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
6643564 TTGGCTAGTC
*
6643574 TATTTAAATTATATTTAT
1 TATTTAAATTATATTTAA
6643592 TATTTAAA-TATATTTACA
1 TATTTAAATTATATTTA-A
6643610 T-TTTAAA
1 TATTTAAA
6643617 ATCAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTAAATTATATTTAA
Found at i:6644169 original size:3 final size:3
Alignment explanation
Indices: 6644161--6644198 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6644151 TTTACTTGGA
6644161 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6644199 GAAGTAGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6645602 original size:4 final size:4
Alignment explanation
Indices: 6645595--6645624 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
6645585 TTCTTAATCT
6645595 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
6645625 TTTTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:6647875 original size:15 final size:15
Alignment explanation
Indices: 6647855--6647928 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
6647845 AGCGCGGGAG
6647855 CAGCAGCAACAGCAA
1 CAGCAGCAACAGCAA
*
6647870 CAGCAGCAGCAGCAA
1 CAGCAGCAACAGCAA
* **
6647885 C--C-TCAACAGCCT
1 CAGCAGCAACAGCAA
*
6647897 CAGCATCAACAGCAA
1 CAGCAGCAACAGCAA
*
6647912 CAGCAGCAGCAGCAA
1 CAGCAGCAACAGCAA
6647927 CA
1 CA
6647929 ACAACTGCAG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
12 7 0.15
13 1 0.02
14 1 0.02
15 38 0.81
ACGTcount: A:0.41, C:0.36, G:0.19, T:0.04
Consensus pattern (15 bp):
CAGCAGCAACAGCAA
Found at i:6647879 original size:21 final size:21
Alignment explanation
Indices: 6647853--6648092 Score: 184
Period size: 21 Copynumber: 11.4 Consensus size: 21
6647843 AAAGCGCGGG
6647853 AGCAGCAGCAACAGCAACAGC
1 AGCAGCAGCAACAGCAACAGC
**
6647874 AGCAGCAGCAACCTCAACAGC
1 AGCAGCAGCAACAGCAACAGC
** *
6647895 CTCAGCATCAACAGCAACAGC
1 AGCAGCAGCAACAGCAACAGC
* *
6647916 AGCAGCAGCAACAACAACTGC
1 AGCAGCAGCAACAGCAACAGC
* * ** * **
6647937 AG-ATGCACCAGCTTCTATTGC
1 AGCA-GCAGCAACAGCAACAGC
*
6647958 AG-AGGCATGCTCAGCAGCAACAGC
1 AGCA-GCA-G--CAACAGCAACAGC
* *
6647982 AGCAGCAACAGCAGCAACAGC
1 AGCAGCAGCAACAGCAACAGC
6648003 AGCAGCAGCAACAGCAACAGC
1 AGCAGCAGCAACAGCAACAGC
*
6648024 AGCAGCAG---CAGCAGCAGC
1 AGCAGCAGCAACAGCAACAGC
* *
6648042 AGCAACAGCAACAGCAGCAGC
1 AGCAGCAGCAACAGCAACAGC
* *
6648063 AGCAGCAGCAGCAGCAGCAGC
1 AGCAGCAGCAACAGCAACAGC
**
6648084 CCCAGCAGC
1 AGCAGCAGC
6648093 GAAGGGATGG
Statistics
Matches: 177, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
18 16 0.09
20 1 0.01
21 146 0.82
24 13 0.07
25 1 0.01
ACGTcount: A:0.37, C:0.34, G:0.24, T:0.05
Consensus pattern (21 bp):
AGCAGCAGCAACAGCAACAGC
Found at i:6648092 original size:3 final size:3
Alignment explanation
Indices: 6647969--6648083 Score: 167
Period size: 3 Copynumber: 38.3 Consensus size: 3
6647959 GAGGCATGCT
* * * *
6647969 CAG CAG CAA CAG CAG CAG CAA CAG CAG CAA CAG CAG CAG CAG CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
6648017 CAA CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAA CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
6648065 CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG C
6648084 CCCAGCAGCG
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.39, C:0.34, G:0.27, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:6649890 original size:6 final size:6
Alignment explanation
Indices: 6649879--6649916 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
6649869 GGCTCAGTTG
*
6649879 CAGCAA CAGCAA CAGCAA CTGCAA CAGCAA CAG-AA CAG
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAG
6649917 TAACTCACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.47, C:0.32, G:0.18, T:0.03
Consensus pattern (6 bp):
CAGCAA
Found at i:6659420 original size:21 final size:21
Alignment explanation
Indices: 6659394--6659442 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6659384 CTCAACAATT
*
6659394 TTCTTTTTGTT-TCCTTTTTTC
1 TTCTTTTTCTTCT-CTTTTTTC
* *
6659415 TTCTTTCTCTTCTCTTTTTTT
1 TTCTTTTTCTTCTCTTTTTTC
6659436 TTCTTTT
1 TTCTTTT
6659443 CCTTTTTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (21 bp):
TTCTTTTTCTTCTCTTTTTTC
Found at i:6669881 original size:18 final size:19
Alignment explanation
Indices: 6669844--6669882 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6669834 ATTGATGATT
*
6669844 ATTTTTAATATTATTTTTA
1 ATTTTTAATATTATTGTTA
*
6669863 ATTTTT-ATATTGTTGTTA
1 ATTTTTAATATTATTGTTA
6669881 AT
1 AT
6669883 GTACGTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTTTAATATTATTGTTA
Found at i:6677968 original size:33 final size:33
Alignment explanation
Indices: 6677907--6678106 Score: 129
Period size: 33 Copynumber: 6.2 Consensus size: 33
6677897 AATAGTTTAT
* *
6677907 AATATTATAATCAAAATAA-AAAATATTAAAATAA
1 AATA-TATAAT-ATAATAATAAAAAATTAAAATAA
6677941 AATATATAATATAATAATAAAAAATTAAAAT--
1 AATATATAATATAATAATAAAAAATTAAAATAA
6677972 AA-A-AT-A-A-AAT-ATAAAAAATTAAAAT--
1 AATATATAATATAATAATAAAAAATTAAAATAA
* * *
6677997 -TTATATAATATAGGTAA-AACAAATTAAAATAA
1 AATATATAATATA-ATAATAAAAAATTAAAATAA
* *
6678029 AATATATAATATAAAAAATATATTAAAAATAAAAATAA
1 AATATATAATAT----AATA-ATAAAAAATTAAAATAA
* * * * *
6678067 AATATAAAAAATTATAATAATAAATAAAAATAA
1 AATATATAATATAATAATAAAAAATTAAAATAA
6678100 AATATAT
1 AATATAT
6678107 GACATTAAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 35
0.72 0.09 0.19
Matches are distributed among these distances:
25 16 0.12
26 5 0.04
27 2 0.02
28 2 0.02
29 3 0.02
30 14 0.11
31 3 0.02
32 6 0.05
33 49 0.37
34 7 0.05
36 2 0.02
37 2 0.02
38 22 0.17
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (33 bp):
AATATATAATATAATAATAAAAAATTAAAATAA
Found at i:6678059 original size:20 final size:20
Alignment explanation
Indices: 6678036--6678121 Score: 54
Period size: 20 Copynumber: 4.3 Consensus size: 20
6678026 TAAAATATAT
6678036 AATATAAAAAATATATTAAA
1 AATATAAAAAATATATTAAA
* *
6678056 AATA-AAAATAAAATATAAAA
1 AATATAAAA-AATATATTAAA
* *
6678076 AAT-TATAATAATA-AATAAA
1 AATATA-AAAAATATATTAAA
* *
6678095 AATA-AAATATATGACATTAAA
1 AATATAAA-AAAT-ATATTAAA
6678116 AATATA
1 AATATA
6678122 TTTAAGAGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
18 2 0.04
19 14 0.29
20 21 0.43
21 11 0.22
22 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (20 bp):
AATATAAAAAATATATTAAA
Found at i:6678063 original size:6 final size:6
Alignment explanation
Indices: 6678052--6678101 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
6678042 AAAAATATAT
* *
6678052 TAAAAA TAAAAA TAAAATA TAAAAAA TTATAA TAATAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAA-A T-AAAAA TAAAAA TAA-AAA TAAAAA TAAAA
6678102 TATATGACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 24 0.65
7 9 0.24
8 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
TAAAAA
Done.